Biology subjects

Lagomarsino, M. C.

Publications and source records attributed to Lagomarsino, M. C..

4 recordsLinked to original sources

bioRxiv2024

Insulation of ribosomal promoter activity by Fis, H-NS or a divergent promoter within the packed E. coli genome.

Gene expression in bacterial cells is dependent on a genes position along the genome, mainly because of the effects of neighbouring genes expression, but also because of the local activity of nucleoid proteins, differing levels of DNA supercoiling and changes in gene copy number with growth rate and growth phase. This genome position dependence can be a source of specific regulation, however, in some cases it is necessary to have gene expression insulated from these local effects. Escherichia coli cells express ribosomal RNA from multiple operons found at different sites along the genome. The number of ribosomal operons varies in different strains and correlates with the maximal growth rate. rRNA promoters are under the regulation of Fis, H-NS, DNA supercoiling and ppGpp. These factors are known to result in growth phase and growth rate dependent regulation of gene expression. Here we show that the combined action of Fis and H-NS also provides insulation from the activity of both local and global regulatory factors. Furthermore, our results indicate that the presence of a divergently expressed gene can also act as an insulator revealing a DNA supercoiling gradient from the origin to the terminus. The organisation of ribosomal promoters therefore has been selected to allow for gene duplication independently of the influence of local genome organisation and neighbouring genes activity.

cell biology↗

bioRxiv2023

Direct single-cell observation of a key E. coli cell cycle oscillator

A long-standing hypothesis sees DNA replication control in E. coli as a central cell cycle os-cillator at whose core is the DnaA protein. The consensus is that the activity of the DnaA protein, which is dependent on its nucleotide bound state, is an effector of initiation of DNA replication and a sensor of cell size. However, while several processes are known to regulate DnaA activity as a function of the cell cycle, the oscillations in DnaA expression and DnaA ac-tivity have never been observed at the single cell level, and their correlation with cell volume has yet to be established. In this study, we measured the volume-specific production rate of a reporter protein under control of the dnaAP2 promoter in single cells. By a careful dissection of the effects of DnaA-ATP-and SeqA-dependent regulation, two distinct cell cycle oscilla-tors emerge. The first oscillator, driven by gene dosage, DnaA activity and SeqA repression oscillates synchronously, and shows a causal relationship, with cell size and divisions, sim-ilarly to initiation events. The second one, a reporter of dosage and DnaA activity only, is strongly coupled to cell size, but loses the synchrony and causality properties, suggesting that DnaA activity peaks do not correspond directly to initiation events. These findings suggest that while transcription regulation by DnaA activity performs volume sensing, transient in-hibition of gene expression by SeqA following replication fork passage keeps DnaA activity oscillations in phase with initiation events.

cell biology↗

bioRxiv2021

Volume growth in animal cells is cell cycle dependent and shows additive fluctuations

The way proliferating animal cells coordinate the growth of their mass, volume, and other relevant size parameters is a long-standing question in biology. Studies focusing on cell mass have identified patterns of mass growth as a function of time and cell cycle phase, but little is known about volume growth. To address this question, we improved our fluorescence exclusion method of volume measurement (FXm) and obtained 1700 single-cell volume growth trajectories of HeLa cells. We find that, during most of the cell cycle, volume growth is close to exponential and proceeds at a higher rate in S-G2 than in G1. Comparing the data with a mathematical model, we establish that the cell-to-cell variability in volume growth arises from constant-amplitude fluctuations in volume steps, rather than fluctuations of the underlying specific growth rate. We hypothesize that such "additive noise" could emerge from the processes that regulate volume adaptation to biophysical cues, such as tension or osmotic pressure.

cell biology↗

bioRxiv2021

Drug-induced colorectal cancer persister cells show increased mutation rate

Compelling evidence shows that cancer persister cells limit the efficacy of targeted therapies. However, it is unclear whether persister cells are induced by anticancer drugs, and if their mutation rate quantitatively increases during treatment. Here, combining experimental characterization and mathematical modeling, we show that, in colorectal cancer, persisters are induced by drug treatment and show a 7- to 50-fold increase of mutation rate when exposed to clinically approved targeted therapies. These findings reveal that treatment may influence persistence and mutability in cancer cells and pinpoints new strategies to restrict tumor recurrence.

cancer biology↗